Locus 4171

Sequence ID 3R_DroMel_CAF1
Location 11,331,160 – 11,331,310
Length 150
Max. P 0.998995
window6691 window6692

overview

Window 1

Location 11,331,160 – 11,331,270
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.88
Mean single sequence MFE -29.02
Consensus MFE -26.96
Energy contribution -26.48
Covariance contribution -0.48
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.93
SVM decision value 3.32
SVM RNA-class probability 0.998995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331160 110 - 27905053
AU----CCACCCACACACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUUUUUUAUGCAAUUUGUGCCGGAAAAGCAGGAAUA------C
.(----((............((((.........)))).((((((((.(((((((((.....)))))))))(((..((....))..))).....))))))))......)))...------. ( -26.80)
>DroSec_CAF1 70333 114 - 1
AUCCAUCCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUUUUUUAUGCAAUUUGUGCCGGAAAAGCAGGAAUA------C
.....(((............((((.........)))).((((((((.(((((((((.....)))))))))(((..((....))..))).....))))))))......)))...------. ( -26.80)
>DroSim_CAF1 68552 114 - 1
AUCCAUCCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUUUUUUAUGCAAUUUGUGCCGGAAAAGCAGGAAUA------C
.....(((............((((.........)))).((((((((.(((((((((.....)))))))))(((..((....))..))).....))))))))......)))...------. ( -26.80)
>DroEre_CAF1 65892 116 - 1
AU----CCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGCGCGCGAAAUUUUUCAUGCAAUUUGUGCCGGAAAAGCAGGAAUACCCGCAC
.(----((............((((.........))))....(((((.(((((((((.....)))))))))(((.(((....))).))).....))))))))...((.((....)).)).. ( -32.20)
>DroYak_CAF1 67593 112 - 1
AU----CCAC----CCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGCGCGCGAAAUUUUUCAUGCAAUUUGUGCCGGAAAAGCAGGAAUACUCGUGC
.(----((..----......((((.........))))....(((((.(((((((((.....)))))))))(((.(((....))).))).....))))))))...(((.((....)).))) ( -32.50)
>consensus
AU____CCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUUUUUUAUGCAAUUUGUGCCGGAAAAGCAGGAAUA______C
.................(((((((.........)))).((((((((.(((((((((.....)))))))))(((.(((....))).))).....)))))))).....)))........... (-26.96 = -26.48 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,331,194 – 11,331,310
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.76
Mean single sequence MFE -28.92
Consensus MFE -26.07
Energy contribution -26.03
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.90
SVM decision value 1.76
SVM RNA-class probability 0.976088
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331194 116 - 27905053
GGCGAAGGAAAAUGAAGGAAAAUCCAGCCAGACGACCACCAU----CCACCCACACACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUU
((((((((....((((((....((......)).((......)----)..........))))))))))).)))......(((.((.(.(((((((((.....)))))))))).)).))).. ( -28.00)
>DroSec_CAF1 70367 120 - 1
UGCGAAGGAAAAUGAAGGAAAAUCCAGCCAGACGACCACCAUCCAUCCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUU
.(((((((....((((((....((......)).((......))..............))))))))))).(((((.....)))))...(((((((((.....)))))))))..))...... ( -27.90)
>DroSim_CAF1 68586 120 - 1
GGCGAAGGAAAAUGAAGGAAAAUCCAGCCAGACGACCACCAUCCAUCCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUU
((((((((....((((((....((......)).((......))..............))))))))))).)))......(((.((.(.(((((((((.....)))))))))).)).))).. ( -28.00)
>DroEre_CAF1 65932 116 - 1
AAUGAAGGAAAAUGAAGGGAAACCCAGCCAGACGGCCACCAU----CCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGCGCGCGAAAUU
..((((((........((....))..(((....)))......----...........))))))..(((.(((((.....)))))...(((((((((.....)))))))))....)))... ( -34.00)
>DroYak_CAF1 67633 112 - 1
AAUGAAGGAAAACGAAGGAAAAUCCAGCCAGACGACCACCAU----CCAC----CCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGCGCGCGAAAUU
..((((((.....(((((....((......)).((......)----)...----...))))).))))))(((((.....)))))...(((((((((.....))))))))).......... ( -26.70)
>consensus
AGCGAAGGAAAAUGAAGGAAAAUCCAGCCAGACGACCACCAU____CCACCCACCCACCUUCACCUUCAGCCAGUGACUUUGGCACUGCACUUGAAAAUUUUUUAAGUGUGCGCGAAAUU
...(((((....((((((.......................................))))))))))).(((((.....)))))...(((((((((.....))))))))).......... (-26.07 = -26.03 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:11 2006